[English] 日本語
Yorodumi
- PDB-9kd0: Crystal structure of Bacteroides ovatus KduI2 responsible for met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kd0
TitleCrystal structure of Bacteroides ovatus KduI2 responsible for metabolism of glycosaminoglycan
Components4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
KeywordsISOMERASE / Glycosaminoglycan metabolism / Bacteroides
Function / homology
Function and homology information


5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process / pectin catabolic process / zinc ion binding
Similarity search - Function
5-keto 4-deoxyuronate isomerase / 5-keto-4-deoxyuronate isomerase, N-terminal / KduI/IolB isomerase / KduI/IolB family / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsKouda, Y. / Takase, R. / Mikami, B. / Hashimoto, W.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H04629 Japan
Japan Society for the Promotion of Science (JSPS)18H02166 Japan
Japan Society for the Promotion of Science (JSPS)21H02156 Japan
Yakult Bio-science Foundation Japan
Japan Foundation for Applied Enzymology Japan
Japan Environ and Organic-farming Foundation Japan
CitationJournal: To Be Published
Title: Crystal structure of Bacteroides ovatus KduI2 responsible for metabolism of glycosaminoglycan
Authors: Kouda, Y. / Takase, R. / Mikami, B. / Hashimoto, W.
History
DepositionNov 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase


Theoretical massNumber of molelcules
Total (without water)33,7281
Polymers33,7281
Non-polymers00
Water00
1
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase

A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase


Theoretical massNumber of molelcules
Total (without water)67,4572
Polymers67,4572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)89.416, 72.936, 39.532
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase


Mass: 33728.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_04897 / Production host: Escherichia coli B (bacteria)
References: UniProt: A0AAN3A235, 5-dehydro-4-deoxy-D-glucuronate isomerase
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: PEG monomethyl ether 2000, Calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. obs: 25764 / % possible obs: 99.7 % / Redundancy: 4.58 % / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.106 / Net I/σ(I): 11.54
Reflection shellResolution: 2.91→3.09 Å / Redundancy: 4.17 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.07 / Num. unique obs: 886 / CC1/2: 0.911 / Rrim(I) all: 0.518 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→39.53 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 282 5.02 %RANDOM
Rwork0.2 ---
obs0.2027 5616 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 0 0 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.485
X-RAY DIFFRACTIONf_dihedral_angle_d16.881790
X-RAY DIFFRACTIONf_chiral_restr0.045311
X-RAY DIFFRACTIONf_plane_restr0.003369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.670.28981400.22472646X-RAY DIFFRACTION99
3.67-39.530.24491420.18982688X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more